Variant report

Variant	rs12378906
Chromosome Location	chr9:116810204-116810205
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116499526..116500493-chr9:116809679..116810647,5	MCF-7	breast:
2	chr9:116499446..116500367-chr9:116809713..116810439,3	K562	blood:
3	chr9:116638359..116640217-chr9:116810086..116811628,2	MCF-7	breast:
4	chr9:116808442..116810806-chr9:116812580..116815116,3	MCF-7	breast:
5	chr9:116499548..116500309-chr9:116809727..116810650,3	MCF-7	breast:
6	chr9:116569406..116570272-chr9:116810108..116810697,3	MCF-7	breast:
7	chr9:116810141..116810692-chr9:117067874..117068694,2	MCF-7	breast:
8	chr9:116444226..116445026-chr9:116809967..116810698,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196739	Chromatin interaction
ENSG00000157657	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10116543	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10118282	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10982036	0.89[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10982037	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10982039	0.87[EUR][1000 genomes]
rs10982044	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10982046	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12380714	1.00[GIH][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12555049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1359171	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1359172	0.89[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1408115	0.88[YRI][hapmap]
rs16911753	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1965753	0.83[YRI][hapmap]
rs41277651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7846976	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7856141	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7869264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116766600-116811200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:116785200-116811200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:116785400-116810600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:116787000-116812800	Weak transcription	Primary B cells from cord blood	blood
5	chr9:116792200-116810400	Weak transcription	Thymus	Thymus
6	chr9:116793200-116811200	Weak transcription	Stomach Mucosa	stomach
7	chr9:116793200-116812200	Weak transcription	K562	blood
8	chr9:116793200-116813800	Weak transcription	NHEK	skin
9	chr9:116795200-116821800	Weak transcription	Right Atrium	heart
10	chr9:116796200-116815800	Weak transcription	Small Intestine	intestine
11	chr9:116799000-116811200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:116799200-116811200	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:116799400-116810600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr9:116799400-116810800	Weak transcription	Colonic Mucosa	Colon
15	chr9:116799800-116810600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:116800000-116810800	Weak transcription	Brain Angular Gyrus	brain
17	chr9:116800000-116811200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:116800000-116811200	Weak transcription	Brain Substantia Nigra	brain
19	chr9:116800000-116811200	Weak transcription	Right Ventricle	heart
20	chr9:116800400-116810800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr9:116800800-116810600	Weak transcription	Brain Anterior Caudate	brain
22	chr9:116800800-116811000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:116800800-116811200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:116801000-116810400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr9:116801000-116810400	Weak transcription	Fetal Brain Female	brain
26	chr9:116801000-116810600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr9:116801000-116811200	Weak transcription	Left Ventricle	heart
28	chr9:116801000-116812000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:116801200-116810400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr9:116801200-116810400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr9:116801200-116810800	Weak transcription	Brain Hippocampus Middle	brain
32	chr9:116801400-116810400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr9:116801400-116811000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:116801600-116810400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:116801600-116810400	Weak transcription	Spleen	Spleen
36	chr9:116801600-116810800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:116801600-116811000	Weak transcription	Esophagus	oesophagus
38	chr9:116801600-116811000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:116802400-116810400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:116804400-116816400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:116805800-116813400	Weak transcription	Fetal Brain Male	brain
42	chr9:116806200-116811200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr9:116807400-116814400	Strong transcription	Fetal Lung	lung
44	chr9:116807600-116817200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:116807800-116815200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:116807800-116816200	Strong transcription	Liver	Liver
47	chr9:116808000-116811000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr9:116808400-116816600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:116808600-116811200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:116808600-116817600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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